Christopher Mohr wrote: > In the resulting alignment there is a separation ("/") between the two > chains of the template sequence. But in the sequence of the target there > isn't a separation of course. Do i have to put a separation in the > sequence of the target in the alignment file or in the input file for > the alignment script? Or whats the best way to handle this problem ?
I don't think I quite understand your question, but the usage of chain breaks ("/") in your alignment is simple - if you have a chain break in the target sequence, Modeller will not link the backbone between the residues either side of the break. If this is what you want, put in a chain break, and if not, don't.
Since a chain break is not a "real" residue, you should always align it with another chain break, or a gap, in the template structure(s).
Ben Webb, Modeller Caretaker